I would just like to give some feedback on what I have done so far. I haven't tried Blowery yet as I wanted to explore using HttpCompression within iis 6 to see how it went, or initially whether it would work with .axd files. To test for the compression statistics on my pages I used the Yahoo add-in for Firefox called YSlow. This add-in appears to me to be intuitive and very helpful.
So I had already turned on iis6 httpcompression on windows server 2003, configuring compression for css,js and aspx files amongst others and then established the files that were/were not being compression using YSlow. Needless to say the webResource.axd files were not being compressed, but the other files were.
Then I changed the iis metabase.xml file to include the file extension axd in the HcScriptFileExtensions property. After I restarted iis the test results from YSlow now showed all webResource.axd files being compressed. I am still testing the functionality to check all client side stuff works as expected, but nothing has been broken so far.
I hope this helps other folks